Keybard and Mouse Preferences Not Saving

We have an OS X server running with remote home folders for a number of different users. Some users have enforced preferences on them. However, on accounts that should have no enforced preferences the keyboard and mouse preferences are getting re-set on every login.
For example if I log in and change the middle click on the mighty mouse to expose, and disable spotlight keyboard shortcuts. Log out and log back in again it will have reset itself back to the system defaults. I have checked file permissions on all of the preference files and can't see anything wrong with them.
The two files that I am aware are not being saved which should are: com.apple.com.systempreferences.plist and com.apple.driver.AppleHIDMouse.plist
This is getting really frustrating as I am having to change my keyboard shortcuts every time I log in to my server account. This isn't just one machine either this is a number of our iMacs.

On the server, go to the System/Library/User Template/English.lproj
This is the default user template that the system uses to create a new user home. You can edit this and add .plist's to it. First, on a client computer (I use a master client for my cloning), set the mouse prefs the way you want them. Then, copy the pertinent .plist (for the mouse settings it is: com.apple.driver.AppleHIDMouse.plist)into the System/Library/User Template/English.lproj/Library/Preferences folder. Now, when you create a new home, the mouse is preset the way you want. If you do not want to affect ALL new accounts, then you can still copy the preset .plist into the users home directly (while they are logged off, of course) and get the same effect. Make sure you check the permissions of the .plist after the copy to make sure it is the same as the users. Hope this helps.

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